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When writing the body of your document, you will use the Markdown format.
Markdown is a lightweight markup language that you can use to add formatting elements to plaintext text documents. - Markdown Guide
When you render your Quarto document, Quarto converts the Markdown-formatted text into HTML, LaTeX, etc., depending on the output format you chose.
You can familiarize yourself with Markdown in a couple of minutes using the following link: https://www.markdownguide.org/cheat-sheet/.
| Markdown Syntax | Output |
|---|---|
|
italics and bold |
|
superscript2 / subscript2 |
|
|
|
verbatim code |
| Markdown Syntax | Output |
|---|---|
|
Header 1 |
|
Header 2 |
|
Header 3 |
|
Header 4 |
You can embed named hyperlinks
Simply a direct url like https://quarto.org/
Links to other places in the document.
| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
| 12 | 12 | 12 | 12 |
| 123 | 123 | 123 | 123 |
| 1 | 1 | 1 | 1 |
| Right | Left | Default | Center |
|---|---|---|---|
| 12 | 12 | 12 | 12 |
| 123 | 123 | 123 | 123 |
| 1 | 1 | 1 | 1 |
$ is treated as “inline” maths$$ is a standalone equation$x$ is an equation, $x $ is notThis \(x^2\) is inline
This equation is standalone \[\bar{x} = \frac{1}{n} \sum_{i=1}^{n} x_i\]
Call-out blocks highlight sections of text that interrupt the flow of your regular text. Maybe it’s a definition, a warning, or a sidenote
When rendering your document to HTML, callout blocks are interactive and can be collapsed and opened.
My First Callout Block!
Say things here
Note
Note that there are five types of callouts, including: note, tip, warning, caution, and important.
Warning
Callouts provide a simple way to attract attention, for example, to this warning.
This is important
Danger, callouts will really improve your writing.
Tip with caption
Caution, under construction
Here is something under construction
Expand To Learn About Collapse
This is an example of a ‘folded’ caution callout that can be expanded by the user. You can use `collapse=“true”` to collapse it by default or `collapse=“false”` to make a collapsible callout that is expanded by default.
Go to the Writing/Reference section on the website and refer to the text provided in the Exercise section.
Copy the text into your Quarto document, like an Introduction of sorts, and reformat it with Markdown Syntax
Render the document to HTML.
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Now that we know how to write in Markdown, let’s add some references!
Adding reproducible references happens with BibTex keys. A typical BibTex key might look like as follows:
We will work with with bibliographies in the form of .bib files (BibTeX Bibliographical Database). .bib files are text files which contain a list of references in the form of BibTex keys.
Here is an example of another BibTex key for a reference used in this workshop:
@misc{RMarkdownWritingReproducible,
title = {{RMarkdown} for writing reproducible scientific papers},
url = {https://libscie.github.io/rmarkdown-workshop/handout.html},
urldate = {2023-04-18},
file = {RMarkdown for writing reproducible scientific papers:C\:\\Users\\Moope001\\Zotero\\storage\\SJITSZZI\\handout.html:text/html},
}The typical workflow is as follows:
.bib file through syncing with Zotero desktop and updating the .bib file.@ + reference identifier:
@nash51 OR @RMarkdownWritingReproducible[@nash51] OR [@nash51, @RMarkdownWritingReproducible]Go to the Referencing section on the website and refer to the instructions in the Exercise section.
You will go through the workflow of creating a .bib file that will be automatically updated by Zotero and integrating it with your Quarto document.
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